Biology subjects

Lin, S.

Publications and source records attributed to Lin, S..

At least 235 records · Page 13Linked to original sources

bioRxiv2020

Molecular Modeling Evaluation of the Binding Abilities of Ritonavir and Lopinavir to Wuhan Pneumonia Coronavirus Proteases

Three anti-HIV drugs, ritonavir, lopinavir and darunavir, might have therapeutic effect on coronavirus disease 2019 (COVID-19). In this study, the structure models of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteases, coronavirus endopeptidase C30 (CEP_C30) and papain like viral protease (PLVP), were built by homology modeling. Ritonavir, lopinavir and darunavir were then docked to the models, respectively, followed by energy minimization of the protease-drug complexes. In the simulations, ritonavir can bind to CEP_C30 most suitably, and induce significant conformation changes of CEP_C30; lopinavir can also bind to CEP_C30 suitably, and induce significant conformation changes of CEP_C30; darunavir can bind to PLVP suitably with slight conformation changes of PLVP. It is suggested that the therapeutic effect of ritonavir and lopinavir on COVID-19 may be mainly due to their inhibitory effect on CEP_C30, while ritonavir may have stronger efficacy; the inhibitory effect of darunavir on SARS-CoV-2 and its potential therapeutic effect may be mainly due to its inhibitory effect on PLVP.

biochemistry↗

bioRxiv2020

Selective germline genome edited pigs and their long immune tolerance in Non Human Primates

Organ transplantation is the only curative treatment for patients with terminal organ failure, however, there is a worldwide organ shortage. Genetically modified pig organs and tissues have become an attractive and practical alternative solution for the severe organ shortage, which has been made possible by significant progress in xenotransplantation in recent years. The past several decades witnessed an expanding list of genetically engineered pigs due to technology advancements, however, the necessary combination of genetic modifications in pig for human organ xenotransplantation has not been determined. In the current study, we created a selective germline genome edited pig (SGGEP). The first triple xenoantigens (GGTA, B4GAL, and CAMH) knockout somatic cells were generated to serve as a prototype cells and then human proteins were expressed in the xenoantigen knockout cells, which include human complement system negative regulatory proteins (CD46, CD55, and CD59); human coagulation system negative regulatory proteins thrombomodulin (THBD); tissue factor pathway inhibitor (TFPI); CD39; macrophage negative regulatory proteins (human CD47); and natural killer cell negative regulatory human HLA-E. After the successful establishment of SGGEP by the nuclear tranfer, we engrafted SGGEP skin to NHP, up to 25 days graft survival without immunosuppressive drugs was observed. Because a pig skin graft does not impact the success of a subsequent allograft or autograft or vice versa, thus our SGGEP could have a great potential for clinical value to save severe and large area burn patients and the other human organ failure. Therefore, this combination of specific gene modifications is a major milestone and provides proof of concept to initiate investigator-initiated clinical trials (IITs) in severe burn patients with defined processes and governance measures in place and the other clinical application.

synthetic biology↗

bioRxiv2020

The RNA-binding protein, Rasputin/G3BP, enhances the stability and translation of its target mRNAs

G3BP RNA-binding proteins are important components of stress granules (SGs). Here we analyze the role of Drosophila G3BP, Rasputin (RIN), in unstressed cells, where RIN is not SG associated. Immunoprecipitation followed by microarray analysis identified over 550 mRNAs that copurify with RIN. The mRNAs found in SGs are long and translationally silent. In contrast, we find that RIN-bound mRNAs, which encode core components of the transcription, splicing and translation machinery, are short, stable and highly translated. We show that RIN is associated with polysomes and provide evidence for a direct role for RIN and its human homologs in stabilizing and upregulating the translation of their target mRNAs. We propose that when cells are stressed the resulting incorporation of RIN/G3BPs into SGs sequesters them away from their short target mRNAs. This would downregulate the expression of these transcripts, even though they are not incorporated into stress granules.

genomics↗

bioRxiv2019

Precise temporal regulation of post-transcriptional repressors is required for an orderly Drosophila maternal-to-zygotic transition

In animal embryos the maternal-to-zygotic transition (MZT) hands developmental control from maternal to zygotic gene products. We show that the maternal proteome represents over half of the protein coding capacity of the Drosophila melanogaster genome and that 2% of this proteome is rapidly degraded during the MZT. Cleared proteins include the post-transcriptional repressors Cup, Trailer hitch (TRAL), Maternal expression at 31B (ME31B), and Smaug (SMG). While the ubiquitin-proteasome system is necessary for clearance of all four repressors, distinct E3 ligase complexes target them: the C-terminal to Lis1 Homology (CTLH) complex targets Cup, TRAL and ME31B for degradation early in the MZT; the Skp/Cullin/F-box-containing (SCF) complex targets SMG at the end of the MZT. Deleting the C-terminal 233 amino acids of SMG makes the protein immune to degradation. We show that artificially persistent SMG downregulates the zygotic re-expression of mRNAs whose maternal contribution is cleared by SMG. Thus, clearance of SMG permits an orderly MZT.

developmental biology↗

bioRxiv2019

The assembly of the Drosophila mushroom body circuit and its regulation by Semaphorin 1a

The Drosophila mushroom body (MB) is a learning and memory center in the fly brain. It is the most extensively studied brain structure in insects, but we know little about the molecular and cellular mechanisms underlying assembly of its neural circuit. The MB is composed of around 2200 intrinsic Kenyon cells (KCs), whose axons are bundled to form multiple MB lobes. The MB lobes are innervated by a large number of extrinsic neurons. Twenty types of dopaminergic neurons (DANs) and 21 types of MB output neurons (MBONs) have been identified. Each type of these extrinsic neurons innervates specific compartments or zones in the MB lobes. Here, we characterize the assembly of the MB circuit and reveal several intriguing features of the process. The DANs and MBONs innervate zones in the MB vertical lobes in specific sequential orders. Innervation of DAN axons in some zones precedes that of MBON dendrites, and vice versa in other zones. MBON and DAN innervations are largely independent of each other. Removing one type of extrinsic neuron during early development has a limited effect on the MB lobe innervations of the other type of extrinsic neurons. However, KC axons are essential for zonal elaboration of DAN axons and MBON dendrites. Competition also exists between MB zones for some MBONs, so when the cognate zones for these MBONs are missing, their dendrites are misdirected to other zones. Finally, we identify Semaphorin 1a (Sema1a) as a crucial guidance molecule for MBON dendrites to innervate specific MB lobe zones. Ectopic expression of Sema1a in some DANs is sufficient to re-direct their dendrites to those zones, demonstrating a potential to rewire the MB circuit. Taken together, our work provides an initial characterization of the cellular and molecular mechanisms underlying MB circuit assembly.

developmental biology↗

bioRxiv2019

Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription

Complex organisms are able to rapidly induce select genes among thousands in response to diverse environmental cues. This occurs in the context of large genomes condensed with histone proteins into chromatin. The macrophage response to pathogen sensing, for example, rapidly engages highly conserved signaling pathways and transcription factors (TFs) for coordination of inflammatory gene induction1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a feature of inflammatory genes and, in general, dynamically regulated chromatin and transcription4-7. However, little is known of how chromatin is regulated at rapidly induced genes and what features of H3.3, conserved from yeast to human, might enable rapid and high-level transcription. The amino-terminus of H3.3 contains a unique serine residue as compared with alanine residues found in \"canonical\" H3.1/2. We find that this H3.3-specific serine residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along the gene bodies of rapidly induced response genes in mouse macrophages responding to pathogen sensing. Further, this selective mark of stimulation-responsive genes directly engages histone methyltransferase (HMT) SETD2, a component of the active transcription machinery. Our structure-function studies reveal that a conserved positively charged cleft in SETD2 contacts H3.3S31ph and specifies preferential methylation of H3.3S31ph nucleosomes. We propose that features of H3.3 at stimulation induced genes, including H3.3S31ph, afford preferential access to the transcription apparatus. Our results provide insight into the function of ancestral histone variant H3.3 and the dedicated epigenetic mechanisms that enable rapid gene induction, with implications for understanding and treating inflammation.

biochemistry↗

bioRxiv2019

A Quantitative Proteome Map of the Human Body

Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from 12,627 genes across 32 normal human tissue types prepared by the GTEx project. Known and new tissue specific or enriched proteins (5,499) were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode highly tissue specific proteins. Discordance in the sites of RNA expression and protein detection also revealed potential sites of synthesis and action of protein signaling molecules. Overall, these results provide an extraordinary resource, and demonstrate that understanding protein levels can provide insights into metabolism, regulation, secretome, and human diseases.\n\nSummaryQuantitative proteome study of 32 human tissues and integrated analysis with transcriptome data revealed that understanding protein levels could provide in-depth knowledge to post transcriptional or translational regulations, human metabolism, secretome, and diseases.

systems biology↗

bioRxiv2019

Isolation and Characterization of a Rhizobium Bacterium Associated with the Toxic Dinoflagellate Gambierdiscus balechii

Algae-bacteria associations are increasingly being recognized to be important in shaping the growth of both algae and bacteria. Bacteria belonging to order Rhizobiales are important symbionts of legumes often developing as nodules on plant roots, but have not been widely documented in association with algae. Here, we detected, isolated, and characterized a Rhizobium species from the toxic benthic dinoflagellate Gambierdiscus culture. The sequence of 16S rDNA showed 99% identity with that of Rhizobium rosettiformans. To further characterize the bacterium, we amplified and sequenced a cell wall hydrolase (CWH)-encoding gene; phylogenetic analysis indicated that this sequence was similar to the homologs of Martellela sp. and Hoeflea sp, of order Rhizobiales. We performed PCR using nifH primers to determine whether this bacterium can fix N2; however, the results of sequencing analysis showed that it was closer to chlorophyllide a reductase-encoding gene (bchX), which is similar to nifH. Results of 16S rDNA qPCR showed that compared to that in the early exponential phase, the abundance of this bacterium increased during the late exponential growth phase of Gambierdiscus. When the dinoflagellate culture was subjected to N limitation, the abundance of the bacterium represented by both 16S rDNA and CWH increased. Based on these results and published literature, it is apparent that this Rhizobium bacterium benefits from the association with Gambierdiscus by hydrolyzing and utilizing the extracellular organic matter exudates released by the dinoflagellate. This is the first report of Rhizobium species being associated with dinoflagellates, which will shed light on the algae-bacteria relationships.\n\nIMPORTANCEPhytoplankton are the undisputed primary producers in the aquatic ecosystems and contribute approximately half of the global net primary productivity.\n\nDinoflagellates are one of the most important phytoplankton in the marine ecosystems. Commonly, they do not exist autonomously in the marine environment but rather co-live with many bacteria that interact with dinoflagellates, producing a dynamic microbial ecosystem. Their interactions play a major role in important processes such as carbon fluxes and nutrient regeneration in the ocean, ultimately influencing the global carbon cycle and the climate. Hence, there is a need to understand the association and relationships between dinoflagellates and bacteria. Here, we tried to elucidate these interactions through isolating and characterizing a bacterium from a benthic toxic dinoflagellate culture. Our study is the first report of such bacterium being recorded to be associated with a dinoflagellate in this genus, providing new insights into the dinoflagellate-bacteria association for future research.

microbiology↗

bioRxiv2019

SET8 localization to chromatin flanking DNA damage is dependent on RNF168 ubiquitin ligase

The DNA damage response (DDR) associated post-translational modifications recruit chromatin remodelers, signaling proteins such as 53BP1 and repair factors to chromatin flanking DNA double strand breaks (DSBs) to promote its repair. Although localization of both RNF168 ubiquitin ligase and SET8 methyltransferase at DSBs is essential for 53BP1s recruitment to DSBs, it is unclear if they do so via the same pathways. Here we report that RNF168 mediates SET8s recruitment to DSBs. Depletion of cellular pool of ubiquitin through proteasome inhibition abolished RNF168 and SET8s localization to DNA damage. Knockdown of RNF8 or RNF168 abolished SET8s recruitment to DNA damage. Moreover, RNF168 and SET8 form stable complexes in vivo. Based on these results we propose a model in which SET8, which despite being a pan-chromatin binding protein, can accumulate several folds at chromatin flanking DSBs through tethering to other proteins that specifically localize to chromatin regions with specific modifications.

cell biology↗

bioRxiv2019

Deamidation in Moxetumomab Pasudotox Leading to Conformational Change and Immunotoxin Activity Loss

Asparagine deamidation is a common posttranslational modification in which asparagine is converted to aspartic acid or isoaspartic acid. By introducing a negative charge, deamidation could potentially impact the binding interface and biological activities of protein therapeutics. We identified a deamidation variant in moxetumomab pasudotox, an immunotoxin Fv fusion protein drug derived from a 38-kilodalton (kDa) truncated Pseudomonas exotoxin A (PE38) for the treatment of hairy-cell leukemia. Although the deamidation site, Asn-358, was outside of the binding interface, the modification had a significant impact on the biological activity of moxetumomab pasudotox. Surprisingly, the variant eluted earlier than its unmodified form on anion exchange chromatography, which suggests a higher positive charge. Here we describe the characterization of the deamidation variant with differential scanning calorimetry and hydrogen-deuterium exchange mass spectrometry, which revealed that the Asn-358 deamidation caused the conformational changes in the catalytic domain of the PE38 region. These results provide a possible explanation for why the deamidation affected the biological activity of moxetumomab pasudotox and suggest an approach that can be used for process control to ensure product quality and process consistency.\n\nStatement of SignificanceAsparagine deamidation can have a potentially significant impact on protein therapeutics. Previous studies have revealed that deamidation at a single site significantly reduces the biological activity of moxetumomab pasudotox, a recombinant anti-CD22 immunotoxin developed for the treatment of B-cell malignancies. Surprisingly, despite the fact that deamidation introduced a negative charge, the deamidated variant eluted earlier than its unmodified form on anion exchange chromatography. In order to understand these observations, we isolated the deamidated variant using an anion exchange column and characterized it by differential scanning calorimetry and hydrogen-deuterium exchange mass spectrometry. The results revealed the conformational change caused by the deamidation, which explains the diminished biological activity of the variant and its early elution time on anion exchange chromatography.

biophysics↗

bioRxiv2019

mTORC1 signaling is not essential for the maintenance of muscle mass and function in adult sedentary mice

BackgroundThe balance between protein synthesis and degradation (proteostasis) is a determining factor for muscle size and function. Signaling via the mammalian target of rapamycin complex 1 (mTORC1) regulates proteostasis in skeletal muscle by affecting protein synthesis and autophagosomal protein degradation. Indeed, genetic inactivation of mTORC1 in developing and growing muscle causes atrophy resulting in a lethal myopathy. However, systemic dampening of mTORC1 signaling by its allosteric inhibitor rapamycin is beneficial at the organismal level and increases lifespan. Whether the beneficial effect of rapamycin comes at the expense of muscle mass and function is yet to be established.\n\nMethodsWe conditionally ablated the gene coding for the mTORC1-essential component raptor in muscle fibers of adult mice (iRAmKO). We performed detailed phenotypic and biochemical analyses of iRAmKO mice and compared them with RAmKO mice, which lack raptor in developing muscle fibers. We also used polysome profiling and proteomics to assess protein translation and associated signaling in skeletal muscle of iRAmKO mice.\n\nResultsAnalysis at different time points reveal that, as in RAmKO mice, the proportion of oxidative fibers decreases, but slow-type fibers increase in iRAmKO mice. Nevertheless, no significant decrease in body and muscle mass, or muscle fiber area was detected up to 5 months post-raptor depletion. Similarly, ex vivo muscle force was not significantly reduced in iRAmKO mice. Despite stable muscle size and function, inducible raptor depletion significantly reduced the expression of key components of the translation machinery and overall translation rates.\n\nConclusionsRaptor depletion and hence complete inhibition of mTORC1 signaling in fully-grown muscle leads to metabolic and morphological changes without inducing muscle atrophy even after 5 months. Together, our data indicate that maintenance of muscle size does not require mTORC1 signaling, suggesting that rapamycin treatment is unlikely to negatively affect muscle mass and function.

molecular biology↗

bioRxiv2019

Small molecule inhibition of PIKFYVE kinase rescues gain- and loss-of-function C9ORF72 ALS/FTD disease processes in vivo

The most common known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is a hexanucleotide repeat expansion (HRE) in C9ORF72 that contributes to neurodegeneration by both loss-of-function (decreased C9ORF72 protein levels) and gain-of-function (e.g. dipeptide repeat protein production) mechanisms. Although therapeutics targeting the gain-of-function mechanisms are in clinical development, it is unclear if these will be efficacious given the contribution of C9ORF72 loss-of-function processes to neurodegeneration. Moreover, there is a lack of therapeutic strategies for C9ORF72 ALS/FTD with demonstrated efficacy in vivo. Here, we show that small molecule inhibition of PIKFYVE kinase rescues both loss- and gain-of-function C9ORF72 disease mechanisms in vivo. We find that the reduction of C9ORF72 in mouse motor neurons leads to a decrease in early endosomes. In contrast, treatment with the PIKFYVE inhibitor apilimod increases the number of endosomes and lysosomes. We show that reduced C9ORF72 levels increases glutamate receptor levels in hippocampal neurons in mice, and that apilimod treatment rescues this excitotoxicity-related phenotype in vivo. Finally, we show that apilimod also alleviates the gain-of-function pathology induced by the C9ORF72 HRE by decreasing levels of dipeptide repeat proteins derived from both sense and antisense C9ORF72 transcripts in hippocampal neurons in vivo. Our data demonstrate the neuroprotective effect of PIKFYVE kinase inhibition in both gain- and loss-of-function murine models of C9ORF72 ALS/FTD.

neuroscience↗

bioRxiv2019

Single cell RNA-Seq analysis identifies molecular mechanisms controlling hypothalamic patterning and differentiation.

The hypothalamus is a central regulator of many innate behaviors essential for survival, but the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control hypothalamic development, we have used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across 12 developmental time points between embryonic day 10 and postnatal day 45. This identified genes that delineated clear developmental trajectories for all major hypothalamic cell types, and readily distinguished major regional subdivisions of the developing hypothalamus. By using our developmental dataset, we were able to rapidly annotate previously unidentified clusters from existing scRNA-Seq datasets collected during development, and to identify the developmental origins of major neuronal populations of the ventromedial hypothalamus. We further show that our approach can rapidly and comprehensively characterize mutants that have altered hypothalamic patterning, identifying Nkx2.1 as a negative regulator of prethalamic identity. These data serve as a resource for further studies of hypothalamic development, physiology and dysfunction.

neuroscience↗

bioRxiv2019

Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis within the nematode lineage

Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages.

cell biology↗

bioRxiv2019

The Salt-Inducible Kinase inhibitor YKL-05-099 suppresses MEF2C function and acute myeloid leukemia progression in vivo

Lineage-defining transcription factors (TFs) are compelling targets for leukemia therapy, yet they are among the most challenging proteins to modulate directly with small molecules. We previously used CRISPR screening to identify a Salt-Inducible Kinase 3 (SIK3) requirement for the growth of acute myeloid leukemia (AML) cell lines that overexpress the lineage TF MEF2C. In this context, SIK3 maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), a repressive cofactor of MEF2C. Here, we evaluated whether inhibition of SIK3 with the tool compound YKL-05-099 can suppress MEF2C function and attenuate disease progression in animal models of AML. Genetic targeting of SIK3 or MEF2C selectively suppressed the growth of transformed hematopoietic cells under in vitro and in vivo conditions. Similar phenotypes were obtained when exposing cells to YKL-05-099, which caused cell cycle arrest and apoptosis in MEF2C-expressing AML cell lines. An epigenomic analysis revealed that YKL-05-099 rapidly suppressed MEF2C function by altering the phosphorylation state and nuclear localization of HDAC4. Using a gatekeeper allele of SIK3, we found that the anti-proliferative effects of YKL-05-099 occurred through on-target inhibition of SIK3 kinase activity. Based on these findings, we treated two different mouse models of MLL-AF9 AML with YKL-05-099, which attenuated disease progression in vivo and extended animal survival at well-tolerated doses. These findings validate SIK3 as a therapeutic target in MEF2C-positive AML and provide a rationale for developing drug-like inhibitors of SIK3 for definitive pre-clinical investigation and for studies in human patients with leukemia.\n\nKey PointsAML cells are uniquely sensitive to genetic or chemical inhibition of Salt-Inducible Kinase 3 in vitro and in vivo.\n\nA SIK inhibitor YKL-05-099 suppresses MEF2C function and AML in vivo.

cancer biology↗

bioRxiv2019

Nuclear gene transformation in a dinoflagellate

The lack of a robust gene transformation tool that allows functional testing of the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of fundamental biology in this ecologically important and evolutionarily unique lineage. Here we report the development of a dinoflagellate expression vector, an electroporation protocol, and successful expression of introduced genes in the dinoflagellate Oxyrrhis marina. This protocol, involving the use of Lonzas Nucleofector and a codon optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.

molecular biology↗

bioRxiv2019

Illuminating the dark depths inside coral

The ability to observe in situ 3D distribution and dynamics of endosymbionts in corals is crucial for gaining a mechanistic understanding of coral bleaching and reef degradation. Here, we report the development of a tissue clearing (TC)-coupled light sheet fluorescence microscopy (LSFM) method for 3D imaging of the coral holobiont at single-cell resolution. The initial applications have demonstrated the ability of this technique to provide high space-resolution quantitative information of endosymbiont abundance and distribution within corals. With specific fluorescent probes or assays, TC-LSFM also revealed spatial distribution and dynamics of physiological conditions (such as cell proliferation, apoptosis, and hypoxia response) in both corals and their endosymbionts. This tool is highly promising for in situ and in-depth data acquisition to illuminate coral symbiosis and health conditions in the changing marine environment, providing fundamental information for coral reef conservation and restoration.

microbiology↗

bioRxiv2018

Transcriptomic responses to thermal stress and varied phosphorus conditions in Symbiodinium kawagutii

Symbiodinium species are essential symbionts of tropical reef-building corals and the disruption of their symbiosis with corals as a consequence of seawater warming and other stress conditions leads to the globally widespread coral bleaching. As coral reefs live in the oligotrophic environment, Symbiodinium photosynthesis can also face nutrient stress. How metabolic pathways in Symbiodinium respond to thermal stress and phosphate depletion is poorly understood and underexplored for many species. Here we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation and glycerol-3-phosphate (Gro3P) replacement in S. kawagutii. RNA-seq and bioinformatic analysis were conducted for the above-mentioned three treatments and a control. We identified 221 (2.04%) genes showing no significant differential expression among all conditions, and defined them as \"core\" genes of S. kawagutii, which mostly were in the Gene Ontology terms of catalytic activity and binding. Using algorithms edgeR and NOIseq in combination, we identified a set of differentially expressed genes (DEGs) for each treatment relative to the control. Under heat stress 357 (4.42%) DEGs were found, with predicted roles in active molecular (protein-protein/RNA/DNA) interaction, cell wall modulation and transport (including nutrients, iron, and oxygen). About as many DEGs (396, 4.73%) were identified under P deprivation while nearly double of that (671, 8.05%) were detected under Gro3P utilization; in both cases most of the DEGs were up-regulated and predicted to function in photosystem and defensome. Further KEGG pathway comparison revealed different molecular responses between phosphate deprivation and Gro3P utilization. Catalytic activity and binding seem to be two important core functions in S. kawagutii. The most significant transcriptional response in S. kawagutii to heat stress was regulation of molecular interaction, cell wall modulation, and transport of iron, oxygen, and major nutrients, suggesting that this species uses a unique mechanism to cope with heat stress, possibly conferring thermal tolerance. The greatest transcriptomic impact of phosphate deprivation and Gro3P replacement were the up-regulation of photosystem and defense. This study provides new clues about molecular mechanisms underpinning responses in Symbiodinium to temperature and nutrient stresses, which will generate new hypotheses and set a new framework for future investigations.

microbiology↗